#============================================================#
#               test vector creation                         #
#                                                            #
# add vectors using residue atoms.                           #
#============================================================*

system echo = off
system verbose = false

# set units
#----------
units
units scale  name = mass   uname = reducedMass   value = 10000.0

# open pdb file
#--------------
database open name = rdb  format = pdb  file = rhodamineB.pdb 

# read molecule
#--------------
molecule read  name = m1   database = rdb   type = miscellaneous


# create a some domains
#----------------------
domain create rhodamine = A
domain rhodamine  bonds  atom_color = element  atoms = true  render = line  show = true

domain create rhodamines = A
domain rhodamines  bonds  atom_color = [ 0 1 0 ]  atoms = true  render = line  show = true

#--------------------------------------------------------------#
#                      create bodies                           #
#--------------------------------------------------------------#
body create  name = ground    type = ground
body create  name = rhodamineBody   type = rigid   domain = rhodamine
body create  name = rhodaminesBody  type = static  domain = rhodamines


#--------------------------------------------------------------#
#                      create joints                           #
#--------------------------------------------------------------#

# joint 1
#--------
joint create  name = 1  type = ball  position = rhodamine:A[201]:C23 
joint 1 color = [ 1 0 0 ] msize = 0.01 shading = color show = true
joint 1 bodies = { ground rhodamineBody }

joint create  name = 2  type = ball  position = rhodamines:A[201]:C25 
joint 2 color = [ 1 0 0 ] msize = 0.01 shading = color show = true
joint 2 bodies = { ground rhodamineBody }


#--------------------------------------------------------------#
#                 create a rigid simulation                    #
#--------------------------------------------------------------#

simulation create name = rsim  type = rigid


# add bodies
#-----------
simulation rsim add body = rhodamineBody
simulation rsim add body = rhodaminesBody
simulation rsim add body = ground         
simulation rsim add joint = 1 
simulation rsim add joint = 2 


# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on


# add forces
#-----------
force create  name = force1         \
              type = explicit         \
              point = [ 0 0 0 ]    \
              direction = [ 0.2 0 0 ]  \
              scale = 1.0

simulation rsim add force = force1       \
                    body = rhodamineBody \
                    time = { 0 1000 }



#--------------------------------------------#
# add vectors using atoms of a residue       #
#--------------------------------------------#

vector create  name = vec1           \  
       point1 = rhodamine:A[201]:C9  \ 
       point2 = rhodamine:A[201]:C8  \ 
       point3 = rhodamine:A[201]:C2  \ 
       color = [ 1 0 1 ]             \
       scale = 1.0                   \
       show = true
simulation rsim add geometry = vec1  body = rhodamineBody

vector create  name = vec2           \
       point1 = rhodamines:A[201]:N1  \
       point2 = rhodamines:A[201]:N2  \
       color = [ 1 1 0 ]             \
       scale = 1.0                   \
       show = true
simulation rsim add geometry = vec2  body = rhodaminesBody


# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.02 
simulation  rsim  momentum = on 


# add a measurement
#------------------
measurement  create  name = vang1   type = angle    \
             vector1 = vec1   body1 = rhodamineBody \
             vector2 = vec2   body2 = rhodaminesBody 

simulation rsim add measurement = vang1
simulation rsim  write  measurement = vang1  print = true  file_name = vang1